Staphylococcus aureus prophages are gatekeepers of lipid utilization to control membrane flexibility, bacterial fitness, and antibiotic adaptation

Phages are ubiquitous in bacteria, including clinical Staphylococcus aureus, where Sfi 21/Sa3 phages often integrate into the hlb gene, encoding Hlb sphingomyelinase. The integration acts as a rapid regulatory switch of Hlb production. Our findings suggest that Sfi 21/Sa3 prophages and Hlb activity affect S. aureus fitness by modulating the incorporation of the toxic linoleic acid (C18:2) from serum into the bacterial membrane. This process relies on C18:2 derived from 1,3-diglyceride, facilitated by the FakB1 kinase subunit. Palmitic acid (C16), primarily released from serum through Hlb activity, competes for FakB1. This mechanism contributes to adaptation to AFN-1252, an antibiotic inhibiting the fatty acid synthesis pathway (anti-FASII). Since S. aureus relies on exogenous fatty acids for growth, AFN-1252 treatment leads to increased proportion of membrane C18:2. Moreover, Hlb inhibition, whether via prophage insertion, gene inactivation, or enzyme inhibition, delays S. aureus adaptation, resulting in higher proportionof C18:2 in the membrane. This study sheds light on the role of lipid environments in infections, and may contribute to the accurate prediction of infection risks and therapeutic efficacy. Furthermore, given that both anti-FASII and Hlb inhibitors enhance C18:2 incorporation, they represent potential agents for combined strategies against S. aureus.